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fixes

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This commit is contained in:
dr. M.S. (Matthijs) Berends
2022-09-27 12:16:39 +02:00
parent aa66632934
commit 626757646b
8 changed files with 92 additions and 57 deletions
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8
inst/tinytest/test-mo.R
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@@ -27,7 +27,7 @@ MOs <- subset(microorganisms, !is.na(mo) & nchar(mo) > 3)
expect_identical(as.character(MOs$mo), as.character(as.mo(MOs$mo)))
expect_identical(
as.character(as.mo(c("E. coli", "H. influenzae"))),
as.character(as.mo(c("E. coli", "H. influenzae"), keep_synonyms = FALSE)),
c("B_ESCHR_COLI", "B_HMPHL_INFL")
)
@@ -41,7 +41,7 @@ expect_equal(as.character(as.mo(" B_ESCHR_COLI ")), "B_ESCHR_COLI")
expect_equal(as.character(as.mo("e coli")), "B_ESCHR_COLI") # not Campylobacter
expect_equal(as.character(as.mo("klpn")), "B_KLBSL_PNMN")
expect_equal(as.character(as.mo("Klebsiella")), "B_KLBSL")
expect_equal(as.character(as.mo("K. pneu rhino")), "B_KLBSL_PNMN_RHNS") # K. pneumoniae subspp. rhinoscleromatis
expect_equal(as.character(as.mo("K. pneumo rhino")), "B_KLBSL_PNMN_RHNS") # K. pneumoniae subspp. rhinoscleromatis
expect_equal(as.character(as.mo("Bartonella")), "B_BRTNL")
expect_equal(as.character(as.mo("C. difficile")), "B_CRDDS_DFFC")
expect_equal(as.character(as.mo("L. pneumophila")), "B_LGNLL_PNMP")
@@ -284,12 +284,12 @@ expect_stdout(print(mo_uncertainties()))
# Salmonella (City) are all actually Salmonella enterica spp (City)
expect_equal(
suppressMessages(as.mo(c("Salmonella Goettingen", "Salmonella Typhimurium", "Salmonella Group A"))),
suppressMessages(as.mo(c("Salmonella Goettingen", "Salmonella Typhimurium", "Salmonella Group A"), keep_synonyms = FALSE)),
as.mo(c("Salmonella enterica", "Salmonella enterica", "Salmonella"))
)
# no viruses
expect_equal(as.character(as.mo("Virus")), NA_character_)
expect_equal(as.mo("Virus"), as.mo("UNKNOWN"))
# summary
expect_equal(length(summary(example_isolates$mo)), 6)

11
inst/tinytest/test-mo_property.R
View File

@@ -75,13 +75,10 @@ expect_identical(MOs$fullname, mo_fullname(MOs$fullname, language = "en"))
expect_equal(mo_type("Escherichia coli", language = "de"), "Bakterien")
expect_equal(mo_gramstain("Escherichia coli", language = "nl"), "Gram-negatief")
expect_stdout(print(mo_gramstain("Escherichia coli", language = "en")))
expect_stdout(print(mo_gramstain("Escherichia coli", language = "de")))
expect_stdout(print(mo_gramstain("Escherichia coli", language = "nl")))
expect_stdout(print(mo_gramstain("Escherichia coli", language = "es")))
expect_stdout(print(mo_gramstain("Escherichia coli", language = "pt")))
expect_stdout(print(mo_gramstain("Escherichia coli", language = "it")))
expect_stdout(print(mo_gramstain("Escherichia coli", language = "fr")))
for (l in LANGUAGES_SUPPORTED) {
expect_stdout(print(mo_gramstain("Escherichia coli", language = l)))
print(mo_gramstain("Escherichia coli", language = l))
}
expect_error(mo_gramstain("Escherichia coli", language = "UNKNOWN"))
dutch <- mo_name(microorganisms$fullname[which(microorganisms$fullname %unlike% "unknown|coagulase")], language = "nl") # should be transformable to English again